Cytogenomics

Cytogenomics

1st Edition - May 25, 2021

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  • Editor: Thomas Liehr
  • eBook ISBN: 9780128235805
  • Paperback ISBN: 9780128235799

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Description

Cytogenomics demonstrates that chromosomes are crucial in understanding the human genome and that new high-throughput approaches are central to advancing cytogenetics in the 21st century. After an introduction to (molecular) cytogenetics, being the basic of all cytogenomic research, this book highlights the strengths and newfound advantages of cytogenomic research methods and technologies, enabling researchers to jump-start their own projects and more effectively gather and interpret chromosomal data. Methods discussed include banding and molecular cytogenetics, molecular combing, molecular karyotyping, next-generation sequencing, epigenetic study approaches, optical mapping/karyomapping, and CRISPR-cas9 applications for cytogenomics. The book’s second half demonstrates recent applications of cytogenomic techniques, such as characterizing 3D chromosome structure across different tissue types and insights into multilayer organization of chromosomes, role of repetitive elements and noncoding RNAs in human genome, studies in topologically associated domains, interchromosomal interactions, and chromoanagenesis. This book is an important reference source for researchers, students, basic and translational scientists, and clinicians in the areas of human genetics, genomics, reproductive medicine, gynecology, obstetrics, internal medicine, oncology, bioinformatics, medical genetics, and prenatal testing, as well as genetic counselors, clinical laboratory geneticists, bioethicists, and fertility specialists.

Key Features

  • Offers applied approaches empowering a new generation of cytogenomic research using a balanced combination of classical and advanced technologies
  • Provides a framework for interpreting chromosome structure and how this affects the functioning of the genome in health and disease
  • Features chapter contributions from international leaders in the field

Readership

Active researchers, basic and translational scientists, and clinicians in the areas of human genetics, genomics, reproductive medicine, gynecology, obstetrics, internal medicine, oncology, bioinformatics, medical genetics, and prenatal testing; genetic counselors; bioethicists; fertility specialists clinicians and students of life science, genetics, and medicine

Table of Contents

  • Cover image
  • Title page
  • Table of Contents
  • Copyright
  • Contributors
  • Chapter 1: A definition for cytogenomics - Which also may be called chromosomics
  • Abstract
  • From cytogenetics to cytogenomics
  • A definition of cytogenomics
  • Conclusion
  • Section 1: Technical aspects
  • Chapter 2: Overview of currently available approaches used in cytogenomics
  • Abstract
  • What is cytogenomics?
  • Cytogenomic approaches
  • Conclusion
  • Chapter 3: Cytogenetics
  • Abstract
  • What is cytogenetics?
  • A short history of cytogenetics
  • Material and methods in cytogenetics
  • Advantages and restrictions
  • Applications
  • Conclusion
  • Chapter 4: Molecular cytogenetics
  • Abstract
  • What is molecular cytogenetics?
  • Probes applied in molecular cytogenetics and how to get them
  • Probe-sets applied in molecular cytogenetics
  • Different resolutions in molecular cytogenetics
  • Cytogenomic applications of molecular cytogenetics
  • Conclusion
  • Chapter 5: Molecular combing solutions to characterize replication kinetics and genome rearrangements
  • Abstract
  • Introduction
  • Basic studies on DNA replication
  • Replication kinetic studies by molecular combing
  • Replication kinetic studies in locus-specific manner
  • Genomic Morse Code (GMC) and its applications
  • GMC designs for CNV studies
  • GMC designs for sequence-specific alterations
  • GMC design for gene editing studies
  • Conclusion
  • Chapter 6: Molecular karyotyping
  • Abstract
  • Background
  • Advantages and restrictions
  • Material applied in molecular karyotyping
  • Microarrays in molecular karyotyping
  • Applications
  • Conclusion
  • Chapter 7: Sequencing approaches
  • Abstract
  • Introduction
  • The first generation
  • The second generation
  • Third generation
  • Fourth generation
  • Complementary methods
  • Summary and conclusion
  • Chapter 8: Next-generation cytogenomics: High-resolution structural variation detection by optical genome mapping
  • Abstract
  • Introduction
  • Introduction to Optical Genome Mapping
  • Applications in constitutional cytogenetics
  • Applications in hematological malignancies
  • Application in solid tumors
  • Concluding remarks
  • Chapter 9: Application of CRISPR/Cas9 to visualize defined genomic sequences in fixed chromosomes and nuclei
  • Abstract
  • Funding information
  • Introduction
  • Application of CRISPR-FISH
  • Chapter 10: Approaches for studying epigenetic aspects of the human genome
  • Abstract
  • Acknowledgment
  • Introduction
  • Analysis of DNA methylation
  • Higher-order chromatin structure analysis
  • Analysis of noncoding RNAs
  • Messenger RNA sequencing
  • Concluding remarks
  • Section 2: Current cytogenomic research
  • Chapter 11: Chromoanagenesis phenomena and their formation mechanisms
  • Abstract
  • Introduction
  • An overview of chromoanagenesis phenomena: Definitions and hallmarks
  • Mechanisms for chromoanagenesis occurrence
  • Factors promoting the emergence of chromoanagenesis
  • Conclusion
  • Chapter 12: 3D cytogenomics: Structural variation in the three-dimensional genome
  • Abstract
  • Introduction
  • 3D genome: Hierarchical organization of genetic information in the nucleus
  • Topologically associating domains
  • Techniques to detect chromatin interactions in the nuclear space
  • Features of a Hi-C map
  • Position effects and TADs
  • SVs detection in the 3D genome
  • Clinical application and future perspectives
  • Chapter 13: Multilayer organization of chromosomes
  • Abstract
  • Introduction
  • Experimental approaches to study the internal structure of mitotic chromosomes
  • Chromatin plates in aqueous solution
  • Self-organization of multilayer chromatin
  • Stacked thin layers explain the morphology of bands and chromosome rearrangements
  • Functional implications of multilayered chromosomes
  • Concluding remarks
  • Chapter 14: Nuclear architecture
  • Abstract
  • Background
  • Short history of nucleomics
  • Present insights into nuclear architecture
  • Conclusion
  • Chapter 15: Nuclear stability in early embryo. Chromosomal aberrations
  • Abstract
  • Acknowledgments
  • Introduction
  • The nucleus of the zygote
  • Chromosomal abnormalities
  • Conclusion
  • Chapter 16: Cytogenomic landscape of the human brain
  • Abstract
  • Acknowledgments
  • Introduction to molecular neurocytogenetics/neurocytogenomics
  • Cytogenomic variation in the human brain: Neuronal diversity versus disease
  • Chromosomal organization in the human brain: Is there a postgenomic perspective?
  • Pathway-based analysis of neurocytogenomic landscape
  • Concluding remarks: What is and what should be
  • Chapter 17: Interchromosomal interactions with meaning for disease
  • Abstract
  • Background
  • Methods used in interchromosomal nucleomics
  • Insights from two own studies
  • Outlook
  • Chapter 18: Shaping of genome by long noncoding RNAs
  • Abstract
  • Acknowledgments
  • Introduction
  • Technologies to determine genome-wide RNA-chromatin interactions
  • Nuclear lncRNAs that recruit chromatin modifiers
  • Nuclear lncRNAs that promote long-range chromatin interactions
  • Interchromosomal interactions via subnuclear structures
  • Breast cancer-specific lncRNAs regulate a long-range chromatin interaction
  • Conclusion
  • Chapter 19: Repetitive elements, heteromorphisms, and copy number variants
  • Abstract
  • Background
  • Types of polymorphic DNA
  • Insights and conclusions
  • Chapter 20: Epigenetics
  • Abstract
  • Introduction
  • Epigenetic regulation and chromatin organization
  • The maternal and the paternal genomes are functionally disparate in higher mammals
  • Disturbances of the subcortical maternal complex
  • Conclusion and outlook
  • Subject Index

Product details

  • No. of pages: 428
  • Language: English
  • Copyright: © Academic Press 2021
  • Published: May 25, 2021
  • Imprint: Academic Press
  • eBook ISBN: 9780128235805
  • Paperback ISBN: 9780128235799

About the Editor

Thomas Liehr

A graduate of the Friedrich-Alexander University of Erlangen, Germany, Thomas Liehr became head of the Molecular Cytogenetic group at the Institute of Human Genetics in Jena in 1998. He is a molecular cytogeneticist with a research interest and more than 800 publications on inherited and acquired marker and derivative chromosomes, karyotype evolution, epigenetics including uniparental disomy, interphase architecture, heterochromatin, and probe set developments. In addition to being in the Editorial Board of the Journal of Histochemistry and Cytochemistry, Dr. Liehr is on the Editorial Board of 16 other journals including the European Journal of Medical Genetics (EJMG) and Oncology Letters. Also, he is the Editor of the online journal Molecular Cytogenetics and has edited seven special issues for different journals. He is a past recipient of the Research Award for Young Scientists of the Friedrich-Schiller University, Jena, invited professor and honorary doctor at Yerevan State University, Armenia, and invited professor at Belgrade Medical School, Serbia. Also, he received the Golden Medal of the Yerevan State University in 2014, Golden Medal of the Research Center for Medical Genetics in 2019, and Medal in memory of Prof. Yuri Yurov in 2019 (see also http://cs-tl.de/TL.html).

Affiliations and Expertise

Professor, Friedrich-Schiller University of Jena, Germany

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